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Several animals in one Anipose file - #172
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Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01N7hYfMaQFqSMBtq9ZWJ3gV
The project hash dumped folder paths with the platform separator, so the two golden-hash tests failed on Windows on every push to main. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01N7hYfMaQFqSMBtq9ZWJ3gV
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Before: An Anipose pose-3d file was read as one animal, so a recording of several animals needed one file each, and group metrics were never offered for native 3-D projects.
After: List the animals' column prefixes in the new
animalsoption (--option animals=fishA,fishB) and the file's<animal>_<keypoint>_x|y|zcolumns become that many animals of one session, in the order given. Without the option nothing changes. Group metrics are offered when every native file of the project lists several animals.The prefixes are named by the user, never guessed, because
left_ear/right_earlook the same asfishA_nose/fishB_nose(decision D-053, option (a) as chosen).How:
readers/anipose.py: theanimalsoption,ANIPOSE_ANIMAL_COLUMNSwhen the columns do not match the list, animal names stored asidentities_labels.metrics/availability.py,readers/native3d.py: group metrics allowed when every native session holds two or more animals.preprocess/identity_switch.py,preprocess/pipeline.py: the step reports the permutation it applied, and the native z follows it, so a corrected swap keeps each animal's height. This replaces the old warning that z could end up on the wrong animal.Tests: reader tests for two animals, order, underscores in prefixes, mismatched columns and cutoffs; gating tests for several-animal, one-animal and mixed projects; an end-to-end add and run with GL-16; a pipeline test that z stays with its animal after a swap. Full suite: 4787 passed, 219 skipped; ruff clean. Synthetic files only, like the rest of the reader.
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